The complete chloroplast genome of Rubus pacificus (Rosaceae)

Abstract The complete chloroplast genome of Rubus pacificus, a representative species of R. sect. Malachobatus subsect. Stipulosi, has been characterized by reference-based assembly using Illumina paired-end data. The complete chloroplast genome is 156,255 bp in length, containing a large single-copy region (LSC) of 85,864 bp and a small single-copy region (SSC) of 18,849 bp, which are separated by a pair of inverted repeat regions (IR) of 25,771 bp. A total of 129 genes were predicted from the chloroplast genome, including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. According to the present sampling, phylogenetic analysis reveals that R. pacificus and R. laciniatostipulatus form a strongly supported clade and R. sect. Malachobatus subsect. Stipulosi is not monophyletic.

Rubus L. sect. Malachobatus Focke subsect. Stipulosi Yu and Lu (1982) contains approximately six species that occur in China. Morphologically, this subsection is characterized by shrubs, leaves simple, stipules and bracts free, broader, usually 2-5 Â 1-2 cm. The genetic relationship of this subsection relative to other Rubus species is poorly understood. Rubus pacificus Hance (1874) is a representative species of R. sect. Malachobatus subsect. Stipulosi. In this study, we first reported the complete chloroplast genome of R. pacificus to examine the phylogenetic relationships of R. sect. Malachobatus subsect. Stipulosi and other Rubus species.
The total genomic DNA was extracted from fresh leaves using a modified CTAB method (Doyle and Doyle 1987) and sequenced based on the Illumina pair-end technology by Novogene Bioinformatics Technology Co., Ltd., Beijing, China. A total of 3.91 Gb clean reads were assembled using the programme GetOrganelle v1.7.5 (Jin et al. 2020) with the complete chloroplast genome of Rubus crassifolius as the reference (GenBank accession No. NC_056941). The assembled chloroplast genome was annotated using PGA (Qu et al. 2019), and the annotation result was modified using Geneious Prime 2020 (Biomatters Ltd., Auckland, New Zealand). Phylogenetic analysis including R. pacificus, 31 other Rubus species (with published plastid genomes) and two outgroups were performed using complete chloroplast genomes. The sequences were aligned using the MAFFT v7.490 (Katoh and Standley 2013). Poorly aligned regions were trimmed using Gblocks v.0.91b (Castresana 2000) with the parameters The maximum-likelihood (ML) tree was constructed using RAxML v.8.2.12 (Stamatakis 2014) with 1000 bootstrap replicates to examine the phylogenetic position of R. pacificus in genus Rubus.
The complete chloroplast genome of Rubus pacificus (Genbank accession No. ON243759) was a circular molecular genome with a size of 156,255 bp in length, which presented a typical quadripartite structure containing a pair of inverted repeat (IR) regions of 25,771 bp each, separated by the large single-copy (LSC) region of 85,864 bp, and small single-copy (SSC) region of 18,849 bp. The overall GC content was about 37.17%. The chloroplast genome consists of 129 genes including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes.

Ethics statement
Plant material was collected in accordance with local permissions and national regulations. The field studies did not involve endangered or protected species.

Author contributions
XX and XL contributed to the conception and design of the study. ZL, CL, CZ and XL performed laboratory work and bioinformatics analyses. XX wrote the first version of the manuscript. All authors read, discussed, and approved the final version and agree to be accountable for all aspects of the work.

Disclosure statement
No potential conflict of interest was reported by the author(s).

Data availability statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov under the accession no. ON243759. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA845828, SRR19542941 and SAMN28863898 respectively.